EBNA1BP2

EBNA1 binding protein 2, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 1:43164174-43270936

Links

ENSG00000117395 ∙ NCBI:10969 ∙ OMIM:614443 ∙ HGNC:15531 ∙ Uniprot:Q99848 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EBNA1BP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EBNA1BP2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			10		2	12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	2

Variants in EBNA1BP2

This is a list of pathogenic ClinVar variants found in the EBNA1BP2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-43164487-G-A		not specified	Uncertain significance (Apr 22, 2022)
1-43164644-T-A			Benign (Dec 31, 2019)
1-43164728-C-T		not specified	Uncertain significance (Jun 10, 2024)
1-43166914-A-G		not specified	Uncertain significance (Aug 08, 2022)
1-43167228-G-A		not specified	Uncertain significance (Aug 04, 2021)
1-43169024-C-T		not specified	Uncertain significance (Dec 13, 2023)
1-43170782-C-T		not specified	Uncertain significance (Mar 29, 2022)
1-43170828-C-A		not specified	Uncertain significance (Aug 02, 2023)
1-43170868-G-A		not specified	Uncertain significance (May 20, 2024)
1-43171494-T-G		not specified	Uncertain significance (Sep 21, 2021)
1-43171575-G-C			Benign (Dec 11, 2018)
1-43171909-G-T		not specified	Uncertain significance (May 22, 2023)
1-43171963-C-G		not specified	Uncertain significance (Sep 13, 2023)
1-43172103-G-C		not specified	Uncertain significance (Oct 03, 2022)
1-43172417-T-C		not specified	Uncertain significance (Sep 01, 2021)
1-43172866-G-T		not specified	Uncertain significance (Nov 03, 2023)
1-43172908-C-T		not specified	Uncertain significance (Mar 01, 2024)
1-43181552-G-T		Van der Woude syndrome 2	Benign (Dec 12, 2023)
1-43181564-T-C		not specified	Uncertain significance (Aug 21, 2023)
1-43181575-C-A		not specified	Uncertain significance (May 09, 2023)
1-43181582-G-A		not specified	Uncertain significance (Oct 12, 2021)
1-43181648-C-G		not specified	Uncertain significance (May 31, 2023)
1-43181659-C-T		not specified	Uncertain significance (May 13, 2024)
1-43181660-G-A		not specified	Uncertain significance (Aug 02, 2023)
1-43181665-C-T		not specified	Uncertain significance (Jun 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EBNA1BP2	protein_coding	protein_coding	ENST00000431635	10	106762

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.37e-9	0.576	125557	0	191	125748	0.000760

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.266	200	211	0.948	0.0000109	2361
Missense in Polyphen		32	46.176	0.693		557
Synonymous	0.273	77	80.1	0.961	0.00000426	680
Loss of Function	1.23	17	23.4	0.726	0.00000137	237

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00359	0.00358
Ashkenazi Jewish	0.00	0.00
East Asian	0.00153	0.00152
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000151	0.000149
Middle Eastern	0.00153	0.00152
South Asian	0.000853	0.000850
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for the processing of the 27S pre-rRNA. {ECO:0000250}.

Recessive Scores

• pRec: 0.127

Intolerance Scores

• loftool: 0.942
• rvis_EVS: 0.42
• rvis_percentile_EVS: 76.96

Haploinsufficiency Scores

• pHI: 0.293
• hipred: Y
• hipred_score: 0.568
• ghis: 0.505

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.895

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Ebna1bp2

Zebrafish Information Network

• Gene name: ebna1bp2
• Affected structure: pigment cell
• Phenotype tag: abnormal
• Phenotype quality: quality

Gene ontology

• Biological process: rRNA processing;ribosomal large subunit biogenesis
• Cellular component: nucleus;nucleolus;preribosome, large subunit precursor;nuclear periphery
• Molecular function: RNA binding